Sequence
atgc intronic sequence ATGC exonic sequence...actggtggaagaccatatgctcagtcattttgtgctttgcattttggtggtaacttaaatgctgcttaagtgcttggagagttatttgaactcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g41100.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G179097_T02 (Zea mays), 3'ss of exon 8
actggtggaagaccatatgctcagtcattttgtgctttgcattttggtggtaacttaaatgctgcttaagtgcttggagagttatttgaactcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGG-------------------------
|| | || ||| | | | || | | | | ||| | | || ||| ||| |||||| | |||||||||| |||||| | |||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||
-------------tatgtattcttcaattggg-----tatagttagctacttattta--ttccactcaagagctc--agagtttgtgaaactcactacgattgttgt--ataacacgtctgcagCT-AAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCTGTCAGCTTATTGTACCTAAGTGACTAAATTTTGTGGAGGGCCTTCAAAAGTGTTCATCTCT
upper sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G139038_T03 (Zea mays), 3'ss of exon 8
actggtggaagaccatatgctcagtcattttgtgctttgcattttg--gtggtaacttaa--atgctgcttaagtgcttggagagttatttgaactcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCT------TGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGG-------------------
||||| ||| || | | || | | | | ||| || | || ||| ||| ||||||| | ||||||||||| | |||||| |||||| ||||||||| |||||||||||||||||||||||||| | | ||| | || | | | || | ||||
------------------------tcattatgtactcttcgcttggttatagctagttatttataccactcaagagct--gagagtttgtggaactcactacggttgttgt--atgacacatctgcagCT-AAGCTGTGGCTGCTTCAAGATAGGAAAGTGACAATTTGTGGAGGGCCTTCAAAAGTGTTTTACTAGTGAACCATGGTGGTCAGTGTACTATCCTTGTA
upper sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 8
actggtggaagaccatatgctcagtcattttgtgctttgcattttg--gtggtaacttaa--atgctgcttaagtgcttggagagttatttgaactcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGG-------
||||| ||| || | | || | | | | ||| || | || ||| ||| ||||||| | ||||||||||| | |||||| |||||| ||||||||| |||||||||||||||||||||||||| | || | | | | ||||| | | | ||
------------------------tcattatgtactcttcgcttggttatagctagttatttataccactcaagagct--gagagtttgtggaactcactacggttgttgt--atgacacatctgcagCT-AAGCTGTGGCTGCTTCAAGATAGGAAAGT-GACAATTTGTGGAGGGCC-TTCAAAAGTGTTTTACTAGTGAACCATGGTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29623101|gb|CB628112.1|CB628112EST: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG CTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGG
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... ctcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtggtaacttaaatgctgcttaagtgcttggagagttatttgaactcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGG
aactcac putative branch site (score: 2)
taacttaaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actggtggaagaccatatgctcagtcattttgtgctttgcattttggtggtaacttaaatgctgcttaagtgcttggagagttatttgaactcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
-ctggtgg
- - - - - - -catatgc
- - - - - - - - - - - - - - - - - ctttgca
- - - - - - - - - - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttg